A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson; Jon G. Sanders; Daniel McDonald; Amnon Amir; Joshua Ladau; Kenneth J. Locey; Robert J. Prill; Anupriya Tripathi; Sean M. Gibbons; Gail Ackermann; Jose A. Navas-Molina; Stefan Janssen; Evguenia Kopylova; Yoshiki Vázquez-Baeza; Antonio González; James T. Morton; Siavash Mirarab; Zhenjiang Zech Xu; Lingjing Jiang; Mohamed F. Haroon; Jad Kanbar; Qiyun Zhu; Se Jin Song; Tomasz Kosciolek; Nicholas A. Bokulich; Joshua Lefler; Colin J. Brislawn; Gregory Humphrey; Sarah M. Owens; Jarrad Hampton-Marcell; Donna Berg-Lyons; Valerie McKenzie; Noah Fierer; Jed A. Fuhrman; Aaron Clauset; Rick L. Stevens; Ashley Shade; Katherine S. Pollard; Kelly D. Goodwin; Janet K. Jansson; Jack A. Gilbert; Rob Knight; Jose L. Agosto Rivera; Lisa Al-Moosawi; John Alverdy; Katherine R. Amato; Jason Andras; Largus T. Angenent; Dionysios A. Antonopoulos; Jonathan B. Clayton; Earth Microbiome Project Consortium

doi:10.1038/nature24621

A communal catalogue reveals Earth's multiscale microbial diversity

Luke R. Thompson, Jon G. Sanders, Daniel McDonald, Amnon Amir, Joshua Ladau, Kenneth J. Locey, Robert J. Prill, Anupriya Tripathi, Sean M. Gibbons, Gail Ackermann, Jose A. Navas-Molina, Stefan Janssen, Evguenia Kopylova, Yoshiki Vázquez-Baeza, Antonio González, James T. Morton, Siavash Mirarab, Zhenjiang Zech Xu, Lingjing Jiang, Mohamed F. HaroonJad Kanbar, Qiyun Zhu, Se Jin Song, Tomasz Kosciolek, Nicholas A. Bokulich, Joshua Lefler, Colin J. Brislawn, Gregory Humphrey, Sarah M. Owens, Jarrad Hampton-Marcell, Donna Berg-Lyons, Valerie McKenzie, Noah Fierer, Jed A. Fuhrman, Aaron Clauset, Rick L. Stevens, Ashley Shade, Katherine S. Pollard, Kelly D. Goodwin, Janet K. Jansson, Jack A. Gilbert, Rob Knight, Jose L. Agosto Rivera, Lisa Al-Moosawi, John Alverdy, Katherine R. Amato, Jason Andras, Largus T. Angenent, Dionysios A. Antonopoulos, Jonathan B. Clayton, Earth Microbiome Project Consortium

Biotechnology Institute

Research output: Contribution to journal › Article › peer-review

980 Scopus citations

Abstract

Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

Original language	English (US)
Pages (from-to)	457-463
Number of pages	7
Journal	Nature
Volume	551
Issue number	7681
DOIs	https://doi.org/10.1038/nature24621
State	Published - Nov 23 2017

Bibliographical note

Funding Information:
Acknowledgements We thank J. DeReus for management of information systems; J. Huntley and K. Jepsen for management of sequencing facilities; B. Erickson for administrative assistance; J. Lennon for discussions about macroecological theory; S. Peddada for assistance with effect size calculations; P. L. Buttigieg, C. Mungall, and D. Siegele for assistance with ontologies; A. Rose, A.-S. Roy, A. Bearquiver, B. Cohen, C. Tischer, C. Feh, D. Winkler, E. Jones, E. Angert, F. Blackwolf, G. Martin, H. Schunck, K. Hallinger, L. R. McGuinness, M. Mühling, M. Lombardo, R. Madsen, S. Bowatte, S. Romac, S. Garcia-Houchins, V. Harriman, and W. James for assistance with sample and/or metadata collection; and the following individuals for supporting the project’s founding: A. Scyzrba, A. McHardy, A. Teske, A. Wilke, C. T. Brown, C. Brown, D. Huson, D. Field, D. Evers, D. Wendel, E. Glass, E. Kolke, F. Sun, F. O. Glöckner, G. Kowalchuk, H.-P. Klenk, J. Tiedje, J. Gordon, J. Raes, J. Knight, J. Kostka, J. Heidelberg, J. Eisen, K. E. Wommack, K. Docherty, K. Keegan, K. Konstantindis, M. Bailey, M. Sullivan, N. Desai, N. Kyprides, N. Pace, P. Balaji, R. Gallery, R. Mackelprang, R. O’Dor, R. Ley, T. Vogel, T. Chen, and W. Feng. This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Department of Energy contract DE-AC02-06CH11357), the Australian Research Council, the Tula Foundation, the Samuel Lawrence Foundation, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. Funding for L.R.T. was provided in part by NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) and the Mississippi State University/NOAA Northern Gulf Institute. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche, and Integrated DNA Technologies for in-kind support at various phases of the project.

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Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., Navas-Molina, J. A., Janssen, S., Kopylova, E., Vázquez-Baeza, Y., González, A., Morton, J. T., Mirarab, S., Xu, Z. Z., Jiang, L., ... Earth Microbiome Project Consortium (2017). A communal catalogue reveals Earth's multiscale microbial diversity. Nature, 551(7681), 457-463. https://doi.org/10.1038/nature24621

Thompson, LR, Sanders, JG, McDonald, D, Amir, A, Ladau, J, Locey, KJ, Prill, RJ, Tripathi, A, Gibbons, SM, Ackermann, G, Navas-Molina, JA, Janssen, S, Kopylova, E, Vázquez-Baeza, Y, González, A, Morton, JT, Mirarab, S, Xu, ZZ, Jiang, L, Haroon, MF, Kanbar, J, Zhu, Q, Song, SJ, Kosciolek, T, Bokulich, NA, Lefler, J, Brislawn, CJ, Humphrey, G, Owens, SM, Hampton-Marcell, J, Berg-Lyons, D, McKenzie, V, Fierer, N, Fuhrman, JA, Clauset, A, Stevens, RL, Shade, A, Pollard, KS, Goodwin, KD, Jansson, JK, Gilbert, JA, Knight, R, Agosto Rivera, JL, Al-Moosawi, L, Alverdy, J, Amato, KR, Andras, J, Angenent, LT, Antonopoulos, DA, Clayton, JB & Earth Microbiome Project Consortium 2017, 'A communal catalogue reveals Earth's multiscale microbial diversity', Nature, vol. 551, no. 7681, pp. 457-463. https://doi.org/10.1038/nature24621

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title = "A communal catalogue reveals Earth's multiscale microbial diversity",

abstract = "Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.",

author = "Thompson, {Luke R.} and Sanders, {Jon G.} and Daniel McDonald and Amnon Amir and Joshua Ladau and Locey, {Kenneth J.} and Prill, {Robert J.} and Anupriya Tripathi and Gibbons, {Sean M.} and Gail Ackermann and Navas-Molina, {Jose A.} and Stefan Janssen and Evguenia Kopylova and Yoshiki V{\'a}zquez-Baeza and Antonio Gonz{\'a}lez and Morton, {James T.} and Siavash Mirarab and Xu, {Zhenjiang Zech} and Lingjing Jiang and Haroon, {Mohamed F.} and Jad Kanbar and Qiyun Zhu and Song, {Se Jin} and Tomasz Kosciolek and Bokulich, {Nicholas A.} and Joshua Lefler and Brislawn, {Colin J.} and Gregory Humphrey and Owens, {Sarah M.} and Jarrad Hampton-Marcell and Donna Berg-Lyons and Valerie McKenzie and Noah Fierer and Fuhrman, {Jed A.} and Aaron Clauset and Stevens, {Rick L.} and Ashley Shade and Pollard, {Katherine S.} and Goodwin, {Kelly D.} and Jansson, {Janet K.} and Gilbert, {Jack A.} and Rob Knight and {Agosto Rivera}, {Jose L.} and Lisa Al-Moosawi and John Alverdy and Amato, {Katherine R.} and Jason Andras and Angenent, {Largus T.} and Antonopoulos, {Dionysios A.} and Clayton, {Jonathan B.} and {Earth Microbiome Project Consortium}",

note = "Funding Information: Acknowledgements We thank J. DeReus for management of information systems; J. Huntley and K. Jepsen for management of sequencing facilities; B. Erickson for administrative assistance; J. Lennon for discussions about macroecological theory; S. Peddada for assistance with effect size calculations; P. L. Buttigieg, C. Mungall, and D. Siegele for assistance with ontologies; A. Rose, A.-S. Roy, A. Bearquiver, B. Cohen, C. Tischer, C. Feh, D. Winkler, E. Jones, E. Angert, F. Blackwolf, G. Martin, H. Schunck, K. Hallinger, L. R. McGuinness, M. M{\"u}hling, M. Lombardo, R. Madsen, S. Bowatte, S. Romac, S. Garcia-Houchins, V. Harriman, and W. James for assistance with sample and/or metadata collection; and the following individuals for supporting the project{\textquoteright}s founding: A. Scyzrba, A. McHardy, A. Teske, A. Wilke, C. T. Brown, C. Brown, D. Huson, D. Field, D. Evers, D. Wendel, E. Glass, E. Kolke, F. Sun, F. O. Gl{\"o}ckner, G. Kowalchuk, H.-P. Klenk, J. Tiedje, J. Gordon, J. Raes, J. Knight, J. Kostka, J. Heidelberg, J. Eisen, K. E. Wommack, K. Docherty, K. Keegan, K. Konstantindis, M. Bailey, M. Sullivan, N. Desai, N. Kyprides, N. Pace, P. Balaji, R. Gallery, R. Mackelprang, R. O{\textquoteright}Dor, R. Ley, T. Vogel, T. Chen, and W. Feng. This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Department of Energy contract DE-AC02-06CH11357), the Australian Research Council, the Tula Foundation, the Samuel Lawrence Foundation, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. Funding for L.R.T. was provided in part by NOAA{\textquoteright}s Atlantic Oceanographic and Meteorological Laboratory (AOML) and the Mississippi State University/NOAA Northern Gulf Institute. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche, and Integrated DNA Technologies for in-kind support at various phases of the project. Publisher Copyright: {\textcopyright} 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.",

year = "2017",

month = nov,

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doi = "10.1038/nature24621",

language = "English (US)",

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T1 - A communal catalogue reveals Earth's multiscale microbial diversity

AU - Thompson, Luke R.

AU - Sanders, Jon G.

AU - McDonald, Daniel

AU - Amir, Amnon

AU - Ladau, Joshua

AU - Locey, Kenneth J.

AU - Prill, Robert J.

AU - Tripathi, Anupriya

AU - Gibbons, Sean M.

AU - Ackermann, Gail

AU - Navas-Molina, Jose A.

AU - Janssen, Stefan

AU - Kopylova, Evguenia

AU - Vázquez-Baeza, Yoshiki

AU - González, Antonio

AU - Morton, James T.

AU - Mirarab, Siavash

AU - Xu, Zhenjiang Zech

AU - Jiang, Lingjing

AU - Haroon, Mohamed F.

AU - Kanbar, Jad

AU - Zhu, Qiyun

AU - Song, Se Jin

AU - Kosciolek, Tomasz

AU - Bokulich, Nicholas A.

AU - Lefler, Joshua

AU - Brislawn, Colin J.

AU - Humphrey, Gregory

AU - Owens, Sarah M.

AU - Hampton-Marcell, Jarrad

AU - Berg-Lyons, Donna

AU - McKenzie, Valerie

AU - Fierer, Noah

AU - Fuhrman, Jed A.

AU - Clauset, Aaron

AU - Stevens, Rick L.

AU - Shade, Ashley

AU - Pollard, Katherine S.

AU - Goodwin, Kelly D.

AU - Jansson, Janet K.

AU - Gilbert, Jack A.

AU - Knight, Rob

AU - Agosto Rivera, Jose L.

AU - Al-Moosawi, Lisa

AU - Alverdy, John

AU - Amato, Katherine R.

AU - Andras, Jason

AU - Angenent, Largus T.

AU - Antonopoulos, Dionysios A.

AU - Clayton, Jonathan B.

AU - Earth Microbiome Project Consortium

N1 - Funding Information: Acknowledgements We thank J. DeReus for management of information systems; J. Huntley and K. Jepsen for management of sequencing facilities; B. Erickson for administrative assistance; J. Lennon for discussions about macroecological theory; S. Peddada for assistance with effect size calculations; P. L. Buttigieg, C. Mungall, and D. Siegele for assistance with ontologies; A. Rose, A.-S. Roy, A. Bearquiver, B. Cohen, C. Tischer, C. Feh, D. Winkler, E. Jones, E. Angert, F. Blackwolf, G. Martin, H. Schunck, K. Hallinger, L. R. McGuinness, M. Mühling, M. Lombardo, R. Madsen, S. Bowatte, S. Romac, S. Garcia-Houchins, V. Harriman, and W. James for assistance with sample and/or metadata collection; and the following individuals for supporting the project’s founding: A. Scyzrba, A. McHardy, A. Teske, A. Wilke, C. T. Brown, C. Brown, D. Huson, D. Field, D. Evers, D. Wendel, E. Glass, E. Kolke, F. Sun, F. O. Glöckner, G. Kowalchuk, H.-P. Klenk, J. Tiedje, J. Gordon, J. Raes, J. Knight, J. Kostka, J. Heidelberg, J. Eisen, K. E. Wommack, K. Docherty, K. Keegan, K. Konstantindis, M. Bailey, M. Sullivan, N. Desai, N. Kyprides, N. Pace, P. Balaji, R. Gallery, R. Mackelprang, R. O’Dor, R. Ley, T. Vogel, T. Chen, and W. Feng. This work was supported by the John Templeton Foundation (grant ID 44000, Convergent Evolution of the Vertebrate Microbiome), the W. M. Keck Foundation (DT061413), Argonne National Laboratory (US Department of Energy contract DE-AC02-06CH11357), the Australian Research Council, the Tula Foundation, the Samuel Lawrence Foundation, and the Extreme Science and Engineering Discovery Environment (XSEDE, project number BIO150043), which is supported by National Science Foundation grant number ACI-1053575. Funding for L.R.T. was provided in part by NOAA’s Atlantic Oceanographic and Meteorological Laboratory (AOML) and the Mississippi State University/NOAA Northern Gulf Institute. We thank MO BIO Laboratories, Luca Technologies, Eppendorf, Boreal Genomics, Illumina, Roche, and Integrated DNA Technologies for in-kind support at various phases of the project. Publisher Copyright: © 2017 Macmillan Publishers Limited, part of Springer Nature. All rights reserved.

PY - 2017/11/23

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N2 - Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

AB - Our growing awareness of the microbial world's importance and diversity contrasts starkly with our limited understanding of its fundamental structure. Despite recent advances in DNA sequencing, a lack of standardized protocols and common analytical frameworks impedes comparisons among studies, hindering the development of global inferences about microbial life on Earth. Here we present a meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project. Coordinated protocols and new analytical methods, particularly the use of exact sequences instead of clustered operational taxonomic units, enable bacterial and archaeal ribosomal RNA gene sequences to be followed across multiple studies and allow us to explore patterns of diversity at an unprecedented scale. The result is both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth's microbial diversity.

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A communal catalogue reveals Earth's multiscale microbial diversity

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